Ancestral genome reconstruction is an important step in analyzing the evolution of genomes. Recent progress in sequencing ancient DNA led to the publication of so-called paleogenomes and allows the integration of this sequencing data in genome evolution analysis. However, the assembly of ancient genomes is fragmented because of DNA degradation over time. Integrated phylogenetic assembly addresses the issue of genome fragmentation in the ancient DNA assembly while improving the reconstruction of all ancient genomes in the phylogeny. The fragmented assembly of the ancient genome can be represented as an assembly graph, indicating contradicting ordering information of contigs. In this setting, our approach is to compare the ancient data with extant finished genomes. We generalize a reconstruction approach minimizing the Single-Cut-or-Join rearrangement distance towards multifur-cating trees and include edge lengths to avoid a sparse reconstruction in practice. When also including the additional conflicting ancient DNA data, we can still ensure consistent reconstructed genomes.
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